They had yellow eyes because not only was it mostly anime, but Super Robot mecha (the likes of Mazinger Z, Getter Robo, Combattler V, Voltes V, etc) and even the original Gundam had yellow eyes. So I guess they decided to make it that way.On the other hand, the robots of the Brave series mostly had Green eyes (minus GaoGaiGar who has red eyes).

And when he was facing Galvatron during the end of Armada, curiously enough he had red eyes. Then again, the eye color doesn't matter much in the Unicron Trilogy. It wasn't just Decepticons having red eyes or Autobots having blue eyes...it was more complicated than that. And the Unicron trilogy is traditionally quite different than most other TF media we've seen too.